#!/usr/bin/env python3
#
# ex:ts=4:sw=4:sts=4:et
# -*- tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*-
#
# Security Response Tool Commandline Tool
#
# Copyright (C) 2018-2019  Wind River Systems
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

### Usage Examples (run from top level directory)
# Updating Jira Issues:     ./bin/<app>/srtool_jira<_app>.py -u

##
## THIS IS A JIRA INTEGRATION SCRIPT FOR
## MANAGING AN ORGANIZATION'S SRTOOL INTEGRATION
##
## You can use the "bin/common/srtool_patcher.py" to extend this template
## with your custom changes yet keep in sync with the shared upstream file.
##
## See the example: "bin/acme/srtool_jira_acme.py"
##
## INSTALLATION INSTRUCTIONS AND DOCUMENATION OF THE JIRA PYTHON
## LIBRARIES CAN BE FOUND HERE:
##    https://jira.readthedocs.io
##

### ACME_EXTENSION_BEGIN ###
#
# This is the ACME 'patcher' extension of:
#   'bin/common/srtool_jira_template.py'
#
# To merge edits in common areas to upstream, run:
#   $ ./bin/common/srtool_patcher.py -j bin/acme/patcher.json --merge-custom
# To merge upstream into this custom extension, run:
#   $ ./bin/common/srtool_patcher.py -j bin/acme/patcher.json --merge-original
#
### ACME_EXTENSION_END ###

import os
import sys
import re
import argparse
import sqlite3
import json
from datetime import datetime, date

# load the srt.sqlite schema indexes
dir_path = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
sys.path.insert(0, dir_path)
from common.srt_schema import ORM

# Setup:
master_log = ''
srt_user = ''
srt_passwd = ''
force_update = False

srtDbName = 'srt.sqlite'
srtErrorLog = 'srt_errors.txt'

#
# Load Jira test
#

try:
    from jira import JIRA
except:
    # could be SRTDBG_SKIP_DEFECT_IMPORT
    pass

##
## THESE ARE JIRA INTEGRATION LINKS:
##   The 'production' link is to the main Jira server
##   The 'test' link is to a test Jira server, for example to pre-test defect creation
##   The 'browse' link is how to format the Jira defect lookup link that is passed to the SRTool users
##

# Jira constants: examples
JIRA_PRODUCTION_LINK = 'https://jira.sample.com'
JIRA_BROWSE_LINK_FORMAT = 'http://jira.sample.com/browse/%s'
JIRA_TESTSERVER_LINK = 'https://jira.sampletest.com'
JIRA_NEW_ASSIGNEE = 'kilroy'

### ACME_EXTENSION_BEGIN ###
JIRA_PRODUCTION_LINK = 'https://jira.wrs.com'
JIRA_BROWSE_LINK_FORMAT = 'http://jira.wrs.com/browse/%s'
JIRA_TESTSERVER_LINK = 'http://jiratest.wrs.com'
JIRA_NEW_ASSIGNEE = 'dreyna'
### ACME_EXTENSION_END ###

##
## THESE ARE SAMPLE JIRA CUSTOM FIELD LINKS:
##   These are example links that you can use to define and populate the respective fields for the SRTool
##   These are not defined in the standard Jira schema, and would presumably be custom added
##   You can extend and cusomize the Jira integration to SRTool by added additional custom fields using this model
## The two indicated fields below are part of the SRTool design. They can be present as empty strings if they
## do not exist in your schema:
##   The 'PUBLISHED' field is used to indicate if and when a Jira defect has been published to the customers
##   The 'FIX_VERSION' field is used to indicate which version/release/update/service pack of the product has the fix
##

# Custom Jira fields
# Custom Jira fields
JIRA_PUBLISHED_FIELD = 'customfield_10001'      ### REPLACE WITH YOUR CUSTOM FIELD VALUE
JIRA_FIX_VERSION_FIELD = 'customfield_10002'    ### REPLACE WITH YOUR CUSTOM FIELD VALUE
# ...

### ACME_EXTENSION_BEGIN ###
JIRA_PUBLISHED_FIELD = 'customfield_10010'
JIRA_FIX_VERSION_FIELD = 'customfield_11002'
### ACME_EXTENSION_END ###

#################################
# Helper methods
#

verbose = False

def debugMsg(msg):
    if verbose:
        print(msg)

overrides = {}

def set_override(key,value=None,quite=False):
    if not value is None:
        overrides[key] = value
    elif key in os.environ.keys():
        overrides[key] = 'yes' if os.environ[key].startswith('1') else 'no'
    else:
        overrides[key] = 'no'
    if 'yes' == overrides[key] and not quite:
        print("OVERRIDE: %s = %s" % (key,overrides[key]))

def get_override(key):
    if key in overrides.keys():
        return 'yes' == overrides[key]
    return False

def srt_error_log(msg):
    f1=open(srtErrorLog, 'a')
    f1.write("|" + msg + "|\n" )
    f1.close()

def get_tag_key(tag,key):
    d = json.loads(tag)
    return d[key]

#################################
# class to hold fields of a Jira issues
#

class Defect():
    project = ''
    product_id = ''
    id = -1
    name = ''
    summary = ''
    url = ''
    priority = -1
    status = ''
    resolution = 'Unresolved'
    publish = ''
    # RCPL
    release_version = ''
    date_created = ''
    date_updated = ''
    # extra fields
    cve_status = ''
    vi_status  = ''
    vi_outcome  = ''

#################################
# import Jira states
#
#if too slow, change to check update times and ignore those that need nothing (should do anyway to be honest...)
#can also move parsing JSON so that it doesnt happen if record is up to date

def do_update_jira():
    try:
        jira = JIRA(JIRA_PRODUCTION_LINK, auth=(srt_user, srt_passwd))
    except Exception as e:
        print("CONNECTION TO JIRA FAILED")
        return 1

    conn = sqlite3.connect(srtDbName)
    c = conn.cursor()

    today = datetime.today()
    weeknum = today.strftime("%W")
    weekday = today.isoweekday()

    update_log = open("./update_logs/update_jira_log_%s_%s.txt" % (weeknum, weekday), "a")

    update_log.write("BEGINNING JIRA UPDATES\n")
    pre_update_time = datetime.now()

    products = c.execute('''SELECT * FROM orm_product''').fetchall()
    for i,product in enumerate(products):
#        print("JIRA_PRODUCT_SCAN:%s,%s" % (product[ORM.PRODUCT_DEFECT_TAGS],get_tag_key(product[ORM.PRODUCT_DEFECT_TAGS],'key')))
        product_defect_prefix = get_tag_key(product[ORM.PRODUCT_DEFECT_TAGS],'key')

        if get_override('SRTDBG_MINIMAL_DB') and (i > 1):
            break

        #specify which fields to get in order to speed up request!
        #print("\tupdating    ...    " + product[ORM.PRODUCT_NAME] + " " + product[ORM.PRODUCT_VERSION] + " " + product[ORM.PRODUCT_PROFILE] + "\tloading " + spinner[block_num % 3], end='\r', flush=True)
        update_log.write("\tUPDATING    ...    " + product[ORM.PRODUCT_NAME] + " " + product[ORM.PRODUCT_VERSION] + " " + product[ORM.PRODUCT_PROFILE] + "\n")

        block_size = 500
        block_num = 0
        spinner = ['   ', '.  ', '.. ', '...']
        while True:
            print("\tloading" + spinner[block_num % 4] + "\t" + product[ORM.PRODUCT_NAME] + " " + product[ORM.PRODUCT_VERSION] + " " + product[ORM.PRODUCT_PROFILE], end='\r', flush=True)
            start_idx = block_num*block_size
            #searches current project's bug issues that contain "cve" in their text
            issues = jira.search_issues('project=%s AND text ~ "cve*" AND type = Bug' % product_defect_prefix, start_idx, block_size, False, fields='key,summary,priority,status,resolution,project,updated,created,%s,%s' % (JIRA_PUBLISHED_FIELD, JIRA_FIX_VERSION_FIELD))
            if len(issues) == 0:
                # Retrieve issues until there are no more to come
                break
            # Development support
            block_num += 1
            update_project_issues(product, issues, conn, update_log)
#            sleep(1.0) # give time for Sqlite to sync
            conn.commit() #commit to db after each block
#            sleep(1.0) # give time for Sqlite to sync
#        conn.commit() #commit to db after each product
        print("\tfinished   \t" + product[ORM.PRODUCT_NAME] + " " + product[ORM.PRODUCT_VERSION] + " " + product[ORM.PRODUCT_PROFILE], flush=True)
    conn.commit()
    update_log.write("began updates: %s\n" % str(pre_update_time))
    update_log.write("finished updates: %s\n" % str(datetime.now()))
    update_log.write("=============================================================================\n")
    update_log.write("\n")

    # Reset datasource's lastModifiedDate as today
    sql = "UPDATE orm_datasource SET lastModifiedDate=? WHERE name='Jira'"
    date_string = datetime.now().strftime(ORM.DATASOURCE_DATETIME_FORMAT)
    ret = c.execute(sql, (date_string,) )
    conn.commit()

    c.close()
    conn.close()

#############################################################################3
###

def new_vulnerability_name(cur):
    sql = "SELECT * FROM orm_srtsetting WHERE name='current_vulnerability_index'"
    cvi = cur.execute(sql).fetchone()
    if not cvi:
        index = 100
        sql = '''INSERT INTO orm_srtsetting (name, helptext, value) VALUES (?,?,?)'''
        cur.execute(sql, ('current_vulnerability_index', '', index))
    else:
        index = int(cvi[ORM.SRTSETTING_VALUE]) + 1
        sql = '''UPDATE orm_srtsetting SET value=? WHERE id = ?'''
        cur.execute(sql, (index, cvi[ORM.SRTSETTING_ID]))
    return "VUL-%05d" % index

def new_investigation_name(cur):
    sql = "SELECT * FROM orm_srtsetting WHERE name='current_investigation_index'"
    cvi = cur.execute(sql).fetchone()
    if not cvi:
        index = 100
        sql = '''INSERT INTO orm_srtsetting (name, helptext, value) VALUES (?,?,?)'''
        cur.execute(sql, ('current_investigation_index', '', index))
    else:
        index = int(cvi[ORM.SRTSETTING_VALUE]) + 1
        sql = '''UPDATE orm_srtsetting SET value=? WHERE id = ?'''
        cur.execute(sql, (index, cvi[ORM.SRTSETTING_ID]))
    return "INV-%05d" % index

def translate_priority(j,p):
    NONE = 0
    MINOR = 1
    LOW = 2
    MEDIUM = 3
    HIGH = 4
    Priority = (
        (NONE, 'None'),
        (MINOR, 'P4'),
        (LOW, 'P3'),
        (MEDIUM, 'P2'),
        (HIGH, 'P1'),
    )

    for i in range(len(Priority)):
        if p == Priority[i][1]:
            return str(Priority[i][0])
    print("ERROR: unknown priority string '%s=%s'" % (j,p))
    srt_error_log("ERROR: unknown priority string '%s=%s'" % (j,p))
    return '0'

def translate_priority_srt_to_jira(s):
    Priority = (
        ('Undefined', 'None'),
        ('Minor', 'P4'),
        ('Low', 'P3'),
        ('Medium', 'P2'),
        ('High', 'P1'),
    )
    for i in range(len(Priority)):
        if s == Priority[i][0]:
            return str(Priority[i][1])
    print("ERROR: unknown priority string '%s'" % (s))
    srt_error_log("ERROR: unknown priority string '%s'" % (s))
    return 'None'

def translate_status(j,s):
    OPEN = 0
    IN_PROGRESS = 1
    ON_HOLD = 2
    CHECKED_IN = 3
    RESOLVED = 4
    CLOSED = 5
    Status = (
        (OPEN, 'Open'),
        (IN_PROGRESS, 'In progress'),
        (ON_HOLD, 'On Hold'),
        (CHECKED_IN, 'Checked In'),
        (RESOLVED, 'Resolved'),
        (CLOSED, 'Closed'),
    )
    for i in range(len(Status)):
        if s == Status[i][1]:
            return str(Status[i][0])
    print("ERROR: unknown status string '%s=%s'" % (j,s))
    srt_error_log("ERROR: unknown status string '%s=%s'" % (j,s))
    return '0'

def translate_resolution(j,r,log):
    Resolution = (
        (ORM.DEFECT_UNRESOLVED, 'Unresolved',                          ORM.STATUS_VULNERABLE,ORM.STATUS_NOT_VULNERABLE,ORM.OUTCOME_OPEN),
        (ORM.DEFECT_RESOLVED, 'Resolved',                              ORM.STATUS_VULNERABLE,ORM.STATUS_NOT_VULNERABLE,ORM.OUTCOME_FIXED),
        (ORM.DEFECT_FIXED, 'Fixed',                                    ORM.STATUS_VULNERABLE,ORM.STATUS_NOT_VULNERABLE,ORM.OUTCOME_FIXED),
        (ORM.DEFECT_WILL_NOT_FIX, 'Won\'t Fix',                        ORM.STATUS_VULNERABLE,ORM.STATUS_NOT_VULNERABLE,ORM.OUTCOME_NOT_FIX),
        (ORM.DEFECT_WITHDRAWN, 'Withdrawn',                            ORM.STATUS_NOT_VULNERABLE,ORM.STATUS_VULNERABLE,ORM.OUTCOME_CLOSED),
        (ORM.DEFECT_REJECTED, 'Rejected',                              ORM.STATUS_NOT_VULNERABLE,ORM.STATUS_VULNERABLE,ORM.OUTCOME_CLOSED),
        (ORM.DEFECT_DUPLICATE, 'Duplicate',                            ORM.STATUS_NOT_VULNERABLE,ORM.STATUS_VULNERABLE,ORM.OUTCOME_CLOSED),
        (ORM.DEFECT_NOT_APPLICABLE, 'Not Applicable',                  ORM.STATUS_NOT_VULNERABLE,ORM.STATUS_VULNERABLE,ORM.OUTCOME_CLOSED),
        (ORM.DEFECT_REPLACED_BY_REQUIREMENT, 'Replaced By Requirement',ORM.STATUS_VULNERABLE,ORM.STATUS_NOT_VULNERABLE,ORM.OUTCOME_CLOSED),
        (ORM.DEFECT_CANNOT_REPRODUCE, 'Cannot Reproduce',              ORM.STATUS_NOT_VULNERABLE,ORM.STATUS_VULNERABLE,ORM.OUTCOME_CLOSED),
        (ORM.DEFECT_DONE, 'Done',                                      ORM.STATUS_VULNERABLE,ORM.STATUS_NOT_VULNERABLE,ORM.OUTCOME_CLOSED),
    )
    for i in range(len(Resolution)):
        if r == Resolution[i][1]:
            return Resolution[i][0],Resolution[i][2],Resolution[i][3],Resolution[i][4],
    print("ERROR: unknown resolution string '%s=%s'" % (j,r))
    log.write("ERROR: unknown resolution string '%s=%s'" % (j,r))
    return 0,0,0,0

#handles updating a list of issues for a single product/project
#DOES NOT CALL COMMIT (should change this?)
def update_project_issues(project, issues, conn, log):
    global force_update

    #CREATE TABLE "orm_defect" (
    #0    "id" integer NOT NULL PRIMARY KEY AUTOINCREMENT
    #1    "name" varchar(50) NOT NULL
    #2    "summary" text NOT NULL
    #3    "url" text NOT NULL
    #4    "priority" integer NOT NULL
    #5    "status" integer NOT NULL
    #6    "resolution" integer NOT NULL
    #7    "publish" text NOT NULL
    #8    "release_version" varchar(50) NOT NULL
    #9    "product_id" integer NULL REFERENCES "orm_product" ("id")
    #10   "date_created" varchar(50) NOT NULL
    #11   "date_updated" varchar(50) NOT NULL);

    USER_SRTOOL_ID = "SRTool"

    project_str = project[ORM.PRODUCT_NAME] + " " + project[ORM.PRODUCT_VERSION] + " " + project[ORM.PRODUCT_PROFILE]
    product_id = project[ORM.PRODUCT_ID]

    cve_regex = re.compile(r"CVE-\d+-\d+")
    srtool_today = datetime.today().strftime('%Y-%m-%d')

    c = conn.cursor()
    d_cursor = conn.cursor()
    for i,issue in enumerate(issues):

        if get_override('SRTDBG_MINIMAL_DB') and (i > 10):
            break

        issue_json = issue.raw

        d = Defect()
        d.project = project_str
        d.product_id = product_id

        d.name = issue_json['key']
        d.date_updated = issue_json['fields']['updated']
        d.date_created = issue_json['fields']['created']
        d.summary = issue_json['fields']['summary']
        d.url = JIRA_BROWSE_LINK_FORMAT % d.name
        d.priority = translate_priority(d.name,issue_json['fields']['priority']['name'])
        d.status = translate_status(d.name,issue_json['fields']['status']['name'])

        if issue_json['fields']['resolution'] is not None:
            d.resolution,cve_status,vi_status,vi_outcome = translate_resolution(d.name,issue_json['fields']['resolution']['name'],log)
        else:
            d.resolution,cve_status,vi_status,vi_outcome = translate_resolution(d.name,'Unresolved',log)
        if JIRA_PUBLISHED_FIELD in issue_json['fields'] and issue_json['fields'][JIRA_PUBLISHED_FIELD] is not None:
            d.publish = issue_json['fields'][JIRA_PUBLISHED_FIELD]['value']
        if JIRA_FIX_VERSION_FIELD in issue_json['fields'] and issue_json['fields'][JIRA_FIX_VERSION_FIELD] is not None:
            d.release_version = issue_json['fields'][JIRA_FIX_VERSION_FIELD]['name']

        sql = "SELECT * FROM orm_defect WHERE name='%s'" % d.name
        defect = c.execute(sql).fetchone()

        #if defect does not exists then create it, if defect is out of date then update the database record, else ignore
        if defect is None:
            log.write("\tINSERTING %s\n" % d.name)
            sql = '''INSERT INTO orm_defect (name, summary, url, priority, status, resolution, publish, release_version, product_id, date_created, date_updated, srt_updated) VALUES (?,?,?,?,?,?,?,?,?,?,?,?)'''
            c.execute(sql, (d.name, d.summary, d.url, d.priority, d.status, d.resolution, str(d.publish), d.release_version, d.product_id, d.date_created, d.date_updated, datetime.now()))
            # Get the new id
            sql = "SELECT * FROM orm_defect WHERE name='%s'" % d.name
            defect = c.execute(sql).fetchone()
            defect_id = defect[ORM.DEFECT_ID]
        elif force_update or (d.date_updated > defect[ORM.DEFECT_DATE_UPDATED]):
            log.write("\tUPDATING %s\n" % d.name)
            sql = '''UPDATE orm_defect SET summary=?, priority=?, status=?, resolution=?, publish=?, release_version=?, date_updated=? WHERE id = ?'''
            c.execute(sql, (d.summary, d.priority, d.status, d.resolution, d.publish, d.release_version, d.date_updated, defect[ORM.DEFECT_ID]))
            defect_id = defect[ORM.DEFECT_ID]
        else:
            log.write("\tSKIPPING %s\n" % d.name)
            continue

        #
        # Update CVE -> Vulnerability -> Investigation -> this Defect chain
        #

        # V/I priority and status minimum from defect
        # Add audit lines

        # Find parent CVE
        m = cve_regex.search(d.summary)
        if m:
            cve_name = m.group(0)
        else:
            print("WARNING: Missing CVE in defect name '%s'" % (d.summary))
            continue
        sql = "SELECT * FROM orm_cve WHERE name='%s'" % cve_name
        cve = c.execute(sql).fetchone()
        if not cve:
            # create the placeholder CVE
            log.write("\tINSERTING CVE for %s\n" % cve_name)
            print("INSERTING CVE for %s,%s" % (cve_name,d.name))

            try:
                a = cve_name.split('-')
                cve_name_sort = '%s-%s-%07d' % (a[0],a[1],int(a[2]))
            except:
                cve_name_sort = cve.name

            sql = ''' INSERT into orm_cve (name, name_sort, priority, status, comments, comments_private, cve_data_type, cve_data_format, cve_data_version, public, publish_state, publish_date, description, publishedDate, lastModifiedDate, recommend, recommend_list, cvssV3_baseScore, cvssV3_baseSeverity, cvssV2_baseScore, cvssV2_severity, packages, srt_updated)
            VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)'''
            c.execute(sql, (cve_name, cve_name_sort, d.priority, cve_status, '', '', '', '', '', 1, 0, '', 'Created from defect %s' % d.name, '', '', 0, '', '', '', '', '', '', datetime.now().strftime(ORM.DATASOURCE_DATETIME_FORMAT)))

            # Find the new id
            print("FINDING CVE ID for %s\n" % cve_name)
            c.execute("SELECT * FROM orm_cve where name = '%s'" % cve_name)
            cve = c.fetchone()
            c_id = cve[ORM.CVE_ID]
            # Also create CVE history entry
            sql = '''INSERT INTO orm_cvehistory (cve_id, comment, date, author) VALUES (?,?,?,?)'''
            c.execute(sql, (c_id,'Created from defect %s' % d.name,srtool_today,USER_SRTOOL_ID))
#            sleep(0.1)
        else:
            c_id = cve[ORM.CVE_ID]

        # Find CVE's vulnerability, else create
        d_cursor.execute("SELECT * FROM orm_cvetovulnerablility where cve_id = '%s'" % c_id)
        c2v = d_cursor.fetchone()
        if not c2v:
            # Create Vulnerability
            v_name = new_vulnerability_name(d_cursor)
            log.write("\tINSERTING VULNERABILITY %s for %s\n" % (v_name,cve_name))
            print("INSERTING VULNERABILITY for (%s,%s)" % (cve_name,v_name))
            sql = '''INSERT INTO orm_vulnerability (name,description,cve_primary_name,public,comments,comments_private,status,outcome,priority) VALUES (?,?,?,?,?,?,?,?,?)'''
            c.execute(sql, (v_name, cve[ORM.CVE_DESCRIPTION], cve_name, True, 'Created from defect %s' % d.name, '', vi_status, vi_outcome ,d.priority))
            # Find the new id
            d_cursor.execute("SELECT * FROM orm_vulnerability where name = '%s'" % v_name)
            v = d_cursor.fetchone()
            v_id = v[ORM.VULNERABILITY_ID]
            # Also create CVE to Vulnerability
            sql = '''INSERT INTO orm_cvetovulnerablility (vulnerability_id, cve_id) VALUES (?,?)'''
            c.execute(sql, (v_id,c_id))
            # Also create Vulnerability history entry
            sql = '''INSERT INTO orm_vulnerabilityhistory (vulnerability_id, comment, date, author) VALUES (?,?,?,?)'''
            c.execute(sql, (v_id,'Created from defect %s' % d.name,srtool_today,USER_SRTOOL_ID))
#            sleep(0.1)
        else:
            print("FOUND VULNERABILITY ID for %s" % (cve_name))
            v_id = c2v[ORM.CVETOVULNERABLILITY_VULNERABILITY_ID]

        # Find CVE's investigation, else create
        sql = "SELECT * FROM orm_investigation where vulnerability_id = '%s' AND product_id = '%s';" % (v_id,d.product_id)
#        print("I_TEST:%s" % sql)
        d_cursor.execute(sql)
        investigation = d_cursor.fetchone()
        if not investigation:
            # Create Investigation
            i_name = new_investigation_name(d_cursor)
            log.write("\tINSERTING INVESTIGATION for %s\n" % cve_name)
            print("INSERTING INVESTIGATION for %s,%s" % (i_name,d.name))
            sql = '''INSERT INTO orm_investigation (name,vulnerability_id,product_id,public,comments,comments_private,status,outcome,priority) VALUES (?,?,?,?,?,?,?,?,?)'''
            c.execute(sql, (i_name, v_id, d.product_id, True, 'Created from defect %s' % d.name, '', vi_status, vi_outcome, d.priority))
            # Find the new id
            d_cursor.execute("SELECT * FROM orm_investigation where name = '%s'" % i_name)
            investigation = d_cursor.fetchone()
            i_id = investigation[ORM.INVESTIGATION_ID]
            # Also create Vulnerability to Investigation
            sql = '''INSERT INTO orm_vulnerabilitytoinvestigation (vulnerability_id, investigation_id) VALUES (?,?)'''
            c.execute(sql, (v_id,i_id))
            # Also create Investigation history entry
            sql = '''INSERT INTO orm_investigationhistory (investigation_id, comment, date, author) VALUES (?,?,?,?)'''
            c.execute(sql, (i_id,'Created from defect %s' % d.name,srtool_today,USER_SRTOOL_ID))
#            sleep(0.1)
        else:
            print("FOUND INVESTIGATION ID for %s" % (cve_name))
            i_id = investigation[ORM.INVESTIGATION_ID]

        # Add this defect to the investigation
        d_cursor.execute("SELECT * FROM orm_investigationtodefect where investigation_id = '%s' and product_id = '%s' and defect_id = '%s'" % (i_id,d.product_id,defect_id))
        i2d = d_cursor.fetchone()
        if not i2d:
            # Create Investigation
            i_name = new_investigation_name(d_cursor)
            log.write("\tINSERTING INVESTIGATION to DEFECT for %s\n" % i_name)
            sql = '''INSERT INTO orm_investigationtodefect (investigation_id, product_id, defect_id) VALUES (?,?,?)'''
            c.execute(sql, (i_id,d.product_id,defect_id))
#            sleep(0.1)

        #print("=========================================================================================\n")
        #print("\n")
    c.close()

#################################
# Jira list update
#

def jira_update_list(jira_list):
    try:
        jira = JIRA(JIRA_PRODUCTION_LINK, auth=(srt_user, srt_passwd))
    except Exception as e:
        print("CONNECTION TO JIRA FAILED")
        return 1

    conn = sqlite3.connect(srtDbName)
    c = conn.cursor()

    products = c.execute('''SELECT * FROM orm_product''').fetchall()
    log = sys.stdout

    for jira_name in jira_list.split(','):
        print("Updating:\t" + jira_name, flush=True)
        # find the matching parent project
        for i,product in enumerate(products):
            product_defect_prefix = get_tag_key(product[ORM.PRODUCT_DEFECT_TAGS],'key')
            print("\tfrom:\t%s %s %s %s" %(product[ORM.PRODUCT_NAME],product[ORM.PRODUCT_VERSION],product[ORM.PRODUCT_PROFILE],product_defect_prefix), flush=True)
            block_size = 500
            block_num = 0
            while True:
                start_idx = block_num*block_size
               #searches current project's bug issues that contain "cve" in their text
                issues = jira.search_issues('project=%s AND text ~ "%s" AND type = Bug' % (product_defect_prefix,jira_name), start_idx, block_size, False, fields='key,summary,priority,status,resolution,project,updated,created,%s,%s' % (JIRA_PUBLISHED_FIELD, JIRA_FIX_VERSION_FIELD))      #project argument could be better written I guess :)
                if len(issues) == 0:
                    # Retrieve issues until there are no more to come
                    break
                # Development support
                block_num += 1
                update_project_issues(product, issues, conn, log)
#               sleep(1.0) # give time for Sqlite to sync
                conn.commit() #commit to db after each block

#################################
# Jira Enhancement Requests
#

#Gets all JIRA Enhancement Requests for the specified project
def get_jira_er(project_prefix):
    print ("GETTING ENHANCEMENT REQUESTS FOR " + project_prefix)
    try:
        jira = JIRA(JIRA_PRODUCTION_LINK, auth=(srt_user, srt_passwd))
    except Exception as e:
        print("CONNECTION TO JIRA FAILED")
        return 1

    block_size = 100
    block_num = 0
    while True:
        start_idx = block_num*block_size
        #searches current project's bug issues that contain "cve" in their text
        issues = jira.search_issues('project=%s AND type = "Enhancement Request"' % project_prefix, start_idx, block_size, False)
        if len(issues) == 0:
            # Retrieve issues until there are no more to come
            break
        block_num += 1
        for issue in issues:
            print (issue.raw['key'])

#################################
# Jira add to investigation
#

def jira_add_to_defect_db(jira_name):
    print("Jira_name=%s" % (jira_name))
    jira_name = jira_name.strip().upper()

    # Just error errors to terminal
    log = sys.stdout

    #try connecting to jira
    try:
        jira = JIRA(JIRA_PRODUCTION_LINK, auth=(srt_user, srt_passwd))
        conn = sqlite3.connect(srtDbName)
        c = conn.cursor()
    except Exception as e:
        print("xhr_investigation_commit:CONNECTION TO JIRA FAILED:(%s)\n" % e, file=sys.stderr)
        return 1

    #Import the issue into the SRTool
    try:
        issue = jira.issue(jira_name, fields='key,summary,priority,status,resolution,project,updated,created,%s,%s' % (JIRA_PUBLISHED_FIELD, JIRA_FIX_VERSION_FIELD))
    except Exception as e:
        print("ERROR:key '%s' does not exist(%s)" % (jira_name,e), file=sys.stderr)
        return 1

    d = Defect()
    try:
        issue_json = issue.raw
        d.name = issue_json['key']
        d.date_updated = issue_json['fields']['updated']
        d.date_created = issue_json['fields']['created']
        d.summary = issue_json['fields']['summary']
        d.url = JIRA_BROWSE_LINK_FORMAT % d.name
        d.priority = translate_priority(d.name,issue_json['fields']['priority']['name'])
        d.status = translate_status(d.name,issue_json['fields']['status']['name'])

        if issue_json['fields']['resolution'] is not None:
            d.resolution,d.cve_status,d.vi_status,d.vi_outcome = translate_resolution(d.name,issue_json['fields']['resolution']['name'],log)
        else:
            d.resolution,d.cve_status,d.vi_status,d.vi_outcome = translate_resolution(d.name,'Unresolved',log)
        if JIRA_PUBLISHED_FIELD in issue_json['fields'] and issue_json['fields'][JIRA_PUBLISHED_FIELD] is not None:
            d.publish = issue_json['fields'][JIRA_PUBLISHED_FIELD]['value']
        else:
            d.publish=''
        if JIRA_FIX_VERSION_FIELD in issue_json['fields'] and issue_json['fields'][JIRA_FIX_VERSION_FIELD] is not None:
            d.release_version = issue_json['fields'][JIRA_FIX_VERSION_FIELD]['name']
        else:
            d.release_version = ''

        # Get the product ID
        products = c.execute('''SELECT * FROM orm_product''').fetchall()
        d.product_id = 1
        for product in products:
            if d.name.startswith(get_tag_key(product[ORM.PRODUCT_DEFECT_TAGS],'key')):
                d.product_id = product[ORM.PRODUCT_ID]
                break

        #_log("\tINSERTING %s\n" % d.name)
        sql = '''INSERT INTO orm_defect (name, summary, url, priority, status, resolution, publish, release_version, product_id, date_created, date_updated) VALUES (?,?,?,?,?,?,?,?,?,?,?)'''
        c.execute(sql, (d.name, d.summary, d.url, d.priority, d.status, d.resolution, str(d.publish), d.release_version, d.product_id, d.date_created, d.date_updated))
        conn.commit()
        c.close()
        conn.close()
    except Exception as e:
        print("ERROR:could not find/import defect(%s)" % e, file=sys.stderr)
        return 1

#################################
# jira_del_from_defect_db
#

# Not yet implemented
def jira_del_from_defect_db(jira_name):
    return 1

#################################
# New defect
#

# Use "jiratest" for development testing
JIRA_IS_TEST = True
JIRA_IS_SIMULATE = True

def simulate_new_defect_name(product_prefix):
    conn = sqlite3.connect(srtDbName)
    cur = conn.cursor()

    sql = "SELECT * FROM orm_srtsetting WHERE name='current_defect_simulation_index'"
    cvi = cur.execute(sql).fetchone()
    if not cvi:
        index = 100
        sql = '''INSERT INTO orm_srtsetting (name, helptext, value) VALUES (?,?,?)'''
        cur.execute(sql, ('current_defect_simulation_index', '', index))
    else:
        index = int(cvi[ORM.SRTSETTING_VALUE]) + 1
        sql = '''UPDATE orm_srtsetting SET value=? WHERE id = ?'''
        cur.execute(sql, (index, cvi[ORM.SRTSETTING_ID]))
    conn.commit() #commit to db
    conn.close()

    defect_name = "%s-%05d" % (product_prefix,index)
    return defect_name

def simulate_new_defect(product_defect_tags,summary,cve_list,description,reason,priority,components,link,jira_url):
    product_defect_prefix = get_tag_key(product_defect_tags,'key')
    defect_name = simulate_new_defect_name(product_defect_prefix)
    print("CREATED:%s,%s/browse/%s" % (defect_name,jira_url,defect_name))

def jira_new_defect(product_defect_tags,summary,cve_list,description,reason,priority,components,link):
    srt_error_log("NEW DEFECT:%s|%s|%s|%s|%s|%s|%s|%s" % (product_defect_tags,summary,cve_list,description,reason,priority,components,link))

    if JIRA_IS_TEST:
        # Test URL
        jira_url = JIRA_TESTSERVER_LINK
    else:
        # Production URL
        jira_url = JIRA_PRODUCTION_LINK

    if JIRA_IS_SIMULATE:
        return simulate_new_defect(product_defect_tags,summary,cve_list,description,reason,priority,components,link,jira_url)

    # Connect to Jira server
    try:
        jira = JIRA(jira_url, auth=(srt_user, srt_passwd))
    except Exception as e:
        print("CONNECTION TO JIRA FAILED")
        return 1
    #srt_error_log("Jira connection made")

    conn = sqlite3.connect(srtDbName)
    c = conn.cursor()

    # append the jira link to description
    description += "\n\n\n%s" % link

    product_defect_prefix = get_tag_key(product_defect_tags,'key')

    # Translate the SRTool priority to Jira priority
    priority = translate_priority_srt_to_jira(priority)

    #print("FOO1:%s,%s,%s" % (product_defect_prefix,summary,description))

    jira_components=list()
    for component in components.split(' '):
        jira_components.append({'name' : component})

    issue_dict = {
        'project': {'key': product_defect_prefix},
        'summary': summary,
        'description': description,
        'issuetype': {'name': 'Bug'},
        'priority': {'name': priority},
        'components': jira_components,             # Components by name
        'assignee': {"name":JIRA_NEW_ASSIGNEE},     # assign to the SRTool developer for now
    }

##
##  Add custom fields here, using the format...
##      issue_dict['custom_field_10001'] = value
##

    ### ACME_EXTENSION_BEGIN ###
    ## HERE IS AN EXAMPLE OF ADJUSTMENTS TO THE JIRA QUERY
    issue_dict['customfield_13304'] = {"value":"Review"}    # "Where Found" = "Review"
    ### ACME_EXTENSION_END ###

    new_issue = jira.create_issue(fields=issue_dict)
    #print("CREATE:%s" % issue_dict)
    #new_issue = '%s-%s' % (product_defect_prefix,datetime.now().strftime('%H%M%S'))

    new_issue = str(new_issue.key)
    if not new_issue.startswith(product_defect_prefix):
        print("ERROR:%s" % new_issue)
    else:
        print("CREATED:%s,%s/browse/%s" % (new_issue,jira_url,new_issue))


def get_projects():
    try:
        jira = JIRA(JIRA_PRODUCTION_LINK, auth=(srt_user, srt_passwd))
    except Exception as e:
        print("CONNECTION TO JIRA FAILED")
        return 1

    # Get all projects viewable by anonymous users.
    projects = jira.projects()
    print("Projects:%s" % projects)


#################################
# Init/Update from Jira status
#

def update_jira(is_init):
    try:
        print("BEGINNING JIRA UPDATES PLEASE WAIT ... this can take some time")
        do_update_jira()
        master_log.write("SRTOOL:%s:DEFECT TABLE & JIRA ISSUES:\t\t\t...\t\t\tUPDATED\n" % (date.today()))
        print("DATABASE UPDATE FINISHED\n")
    except Exception as e:
        master_log.write("SRTOOL:%s:DEFECT TABLE & JIRA ISSUES:\t\t\t...\t\t\tFAILED ... %s\n" % (date.today(), e))
        print("DATABASE UPDATES FAILED ... %s" % e)
        return(1)
    return(0)

#################################
# main loop
#

def main(argv):
    global force_update
    global verbose
    global master_log
    global srt_user
    global srt_passwd

    parser = argparse.ArgumentParser(description='srtool_jira.py: Manage the SRTool to Jira connection')
    parser.add_argument('--init-jira', '-i', action='store_const', const='init_jira', dest='command', help='Init and import Jira states and update defects')
    parser.add_argument('--update-jira', '-u', action='store_const', const='update_jira', dest='command', help='Import Jira states and update defects')
    parser.add_argument('--update-jira-list', '-l', dest='jira_update_list', help='List of Jira defects to update in SRTool database')
    parser.add_argument('--jira_er', '-e', nargs=1, help='Query list of pending ERs under a project, review them, and assign to Rally themes')
    parser.add_argument('--force', '-f', action='store_true', dest='force_update', help='Force updates')
    parser.add_argument('--verbose', '-v', action='store_true', dest='verbose', help='Verbose debugging')
    parser.add_argument('--user', dest='user', help='User name for Jira access')
    parser.add_argument('--passwd', dest='passwd', help='User password for Jira access')

    parser.add_argument('--add', nargs=1, help='Add an existing defect to SRTool defect database')
    parser.add_argument('--delete', nargs=1, help='Delete an existing defect from SRTool defect database')
    parser.add_argument('--new', action='store_const', const='new', dest='command', help='Create a new defect "--new --product-tags --summary --cve --description --reason --priority --components --link"')
    parser.add_argument('--jira-projects', '-j', action='store_const', const='jira-projects', dest='command', help='Jira projects')

    # Be flexible with arguments to support sub-parse trees
    args, argv = parser.parse_known_args()

    master_log = open("./update_logs/master_log.txt", "a")

    if get_override('SRTDBG_SKIP_DEFECT_IMPORT'):
        print("...Skipping Defect import")
        exit(0)

    # Authorization
    if args.user:
        srt_user = args.user
    else:
        srt_user = os.environ.get('SRT_USER')
    if args.passwd:
        srt_passwd = args.passwd
    else:
        srt_passwd = os.environ.get('SRT_PASSWD')
    if not srt_user or not srt_passwd:
        msg = "FATAL ERROR: Missing user/password for Jira access"
        print(msg)
        srt_error_log(msg)
        return 1

    force_update = False
    if None != args.force_update:
        force_update = args.force_update
    if None != args.verbose:
        verbose = True
    if verbose:
        srt_error_log("srtool_jira: NOTE unprocessed arguments: %s" % argv)

    jira_list = ''
    if None != args.jira_update_list:
        jira_list = args.jira_update_list

    ret = 0
    if args.jira_er:
        ret = get_jira_er(args.jira_er[0])
    elif args.add:
        ret = jira_add_to_defect_db(args.add[0])
    elif args.delete:
        ret = jira_del_from_defect_db(args.add[0])
    elif 'new' == args.command:
        # Instantiate a sub-parse tree for "new" specific arguments
        # Example:
        # $ ./bin/<app>/srtool_jira.py --new --product-tags '{"key":"MERRIE"}' --summary 'User error' \
        #   --cve 'CVE-2019-0000' --description 'Incorrect equipement use' --reason 'beep'  \
        #   --priority High --components "acme" --link 'www.acme.com/cve/CVE-2019-0000'
        new_parser = argparse.ArgumentParser(parents=[parser],add_help=False)
        new_parser.add_argument('--product-tags','-T', dest='tags', help='Product tags for defect tool integration')
        new_parser.add_argument('--summary','-S', help='Defect summary')
        new_parser.add_argument('--cve','-C', help='CVE list')
        new_parser.add_argument('--description','-D', help='Defect summary')
        new_parser.add_argument('--reason','-R', help='Defect reason hint')
        new_parser.add_argument('--priority','-P', help='Defect priority')
        new_parser.add_argument('--components','-O', help='Affected components')
        new_parser.add_argument('--link','-L', help='Link to upstream CVE')
        args, argv = new_parser.parse_known_args()
        if verbose:
            srt_error_log("SRTool_Jira:NEW: NOTE unprocessed arguments: %s" % argv)
        jira_new_defect(
            args.tags if args.tags else '{}',
            args.summary if args.summary else '',
            args.cve if args.cve else '',
            args.description if args.description else '',
            args.reason if args.reason else '',
            args.priority if args.priority else '',
            args.components if args.components else '',
            args.link if args.link else '',
            )
    elif 'init_jira' == args.command:
        ret = update_jira(True)
    elif 'update_jira' == args.command:
        ret = update_jira(False)
    elif jira_list:
        ret = jira_update_list(jira_list)
    elif 'jira-projects' == args.command:
        ret = get_projects()
    else:
        print("Command not found")

    if 0 != ret:
        exit(ret)


if __name__ == '__main__':
    if verbose: print("srtool_jira(%s)" % sys.argv[1:])

    # fetch any environment overrides
    set_override('SRTDBG_SKIP_DEFECT_IMPORT')
    set_override('SRTDBG_MINIMAL_DB')

    srtool_basepath = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(sys.argv[0]))))
    main(sys.argv[1:])